Spinal cord data#

Spinal cord CSA#

Code imports#

# Python imports 
from IPython.display import clear_output
from pathlib import Path
import numpy as np
import pandas as pd

# Import custom tools
from tools.data import Data
from tools.plot import Plot

Download data#

data_type = 'spine'
release_version = 'latest'

dataset = Data(data_type)
dataset.download(release_version)
Archive:  spinalcord_results.zip
  inflating: data/spine/DWI_RD.csv   
  inflating: data/spine/DWI_FA.csv   
  inflating: data/spine/csa-SC_T2w.csv  
  inflating: data/spine/DWI_MD.csv   
  inflating: data/spine/MTR.csv      
  inflating: data/spine/MTsat.csv    
  inflating: data/spine/csa-GM_T2s.csv  
  inflating: data/spine/csa-SC_T1w.csv  
  inflating: data/spine/._csa-SC_T1w.csv  
  inflating: data/spine/T1.csv       
--2022-06-14 00:05:36--  https://github.com/courtois-neuromod/anat-processing/releases/download//r20210610/spinalcord_results.zip
Resolving github.com (github.com)... 140.82.114.4
Connecting to github.com (github.com)|140.82.114.4|:443... connected.
HTTP request sent, awaiting response... 302 Found
Location: https://objects.githubusercontent.com/github-production-release-asset-2e65be/333825187/9e444c00-c9e2-11eb-880c-f9aa2a43f100?X-Amz-Algorithm=AWS4-HMAC-SHA256&X-Amz-Credential=AKIAIWNJYAX4CSVEH53A%2F20220614%2Fus-east-1%2Fs3%2Faws4_request&X-Amz-Date=20220614T000536Z&X-Amz-Expires=300&X-Amz-Signature=238f36051ea01c3f5e90af0eedd912c03f7f4e0280c8642b8f16eed6fa829b86&X-Amz-SignedHeaders=host&actor_id=0&key_id=0&repo_id=333825187&response-content-disposition=attachment%3B%20filename%3Dspinalcord_results.zip&response-content-type=application%2Foctet-stream [following]
--2022-06-14 00:05:36--  https://objects.githubusercontent.com/github-production-release-asset-2e65be/333825187/9e444c00-c9e2-11eb-880c-f9aa2a43f100?X-Amz-Algorithm=AWS4-HMAC-SHA256&X-Amz-Credential=AKIAIWNJYAX4CSVEH53A%2F20220614%2Fus-east-1%2Fs3%2Faws4_request&X-Amz-Date=20220614T000536Z&X-Amz-Expires=300&X-Amz-Signature=238f36051ea01c3f5e90af0eedd912c03f7f4e0280c8642b8f16eed6fa829b86&X-Amz-SignedHeaders=host&actor_id=0&key_id=0&repo_id=333825187&response-content-disposition=attachment%3B%20filename%3Dspinalcord_results.zip&response-content-type=application%2Foctet-stream
Resolving objects.githubusercontent.com (objects.githubusercontent.com)... 185.199.110.133, 185.199.109.133, 185.199.108.133, ...
Connecting to objects.githubusercontent.com (objects.githubusercontent.com)|185.199.110.133|:443... connected.
HTTP request sent, awaiting response... 200 OK
Length: 19324 (19K) [application/octet-stream]
Saving to: ‘spinalcord_results.zip’

     0K .......... ........                                   100% 29.7M=0.001s

2022-06-14 00:05:36 (29.7 MB/s) - ‘spinalcord_results.zip’ saved [19324/19324]

Load data plot it#

dataset.load()

fig_spine = Plot(dataset, plot_name = 'spine-1')

fig_spine.title = 'Spinal cord CSA [T<sub>1</sub>w/T<sub>2</sub>w]'
# If you're running this notebook in a Jupyter Notebook (eg, on MyBinder), change 'jupyter-book' to 'notebook'
fig_spine.display('jupyter-book', tissue = 'WM')
{'T1w':    Subject Session            Timestamp  \
1        1       1  2021-06-09 23:24:10   
6        1       2  2021-06-09 23:24:19   
0        1       3  2021-06-09 23:24:08   
8        2       1  2021-06-09 23:41:15   
10       2       2  2021-06-09 23:41:24   
15       2       3  2021-06-09 23:50:43   
12       2       4  2021-06-09 23:41:39   
9        3       1  2021-06-09 23:41:20   
13       3       2  2021-06-09 23:41:42   
11       3       3  2021-06-09 23:41:39   
16       3       4  2021-06-09 23:55:17   
17       4       2  2021-06-09 23:55:38   
18       4       3  2021-06-09 23:55:53   
4        5       1  2021-06-09 23:24:18   
14       5       2  2021-06-09 23:41:45   
2        6       1  2021-06-09 23:24:11   
7        6       2  2021-06-09 23:24:21   
5        6       3  2021-06-09 23:24:19   
3        6       4  2021-06-09 23:24:12   

                                          SCT Version  \
1   git-jca/3413-run-batch-session-c41958db922273a...   
6   git-jca/3413-run-batch-session-c41958db922273a...   
0   git-jca/3413-run-batch-session-c41958db922273a...   
8   git-jca/3413-run-batch-session-c41958db922273a...   
10  git-jca/3413-run-batch-session-c41958db922273a...   
15  git-jca/3413-run-batch-session-c41958db922273a...   
12  git-jca/3413-run-batch-session-c41958db922273a...   
9   git-jca/3413-run-batch-session-c41958db922273a...   
13  git-jca/3413-run-batch-session-c41958db922273a...   
11  git-jca/3413-run-batch-session-c41958db922273a...   
16  git-jca/3413-run-batch-session-c41958db922273a...   
17  git-jca/3413-run-batch-session-c41958db922273a...   
18  git-jca/3413-run-batch-session-c41958db922273a...   
4   git-jca/3413-run-batch-session-c41958db922273a...   
14  git-jca/3413-run-batch-session-c41958db922273a...   
2   git-jca/3413-run-batch-session-c41958db922273a...   
7   git-jca/3413-run-batch-session-c41958db922273a...   
5   git-jca/3413-run-batch-session-c41958db922273a...   
3   git-jca/3413-run-batch-session-c41958db922273a...   

                                             Filename Slice (I->S) VertLevel  \
1   /Users/julien/temp/neuromod/data_processed/sub...        31:75       2:3   
6   /Users/julien/temp/neuromod/data_processed/sub...        47:86       2:3   
0   /Users/julien/temp/neuromod/data_processed/sub...        51:93       2:3   
8   /Users/julien/temp/neuromod/data_processed/sub...         1:38       2:3   
10  /Users/julien/temp/neuromod/data_processed/sub...        12:50       2:3   
15  /Users/julien/temp/neuromod/data_processed/sub...         3:39       2:3   
12  /Users/julien/temp/neuromod/data_processed/sub...         9:46       2:3   
9   /Users/julien/temp/neuromod/data_processed/sub...        51:85       2:3   
13  /Users/julien/temp/neuromod/data_processed/sub...        33:66       2:3   
11  /Users/julien/temp/neuromod/data_processed/sub...        43:77       2:3   
16  /Users/julien/temp/neuromod/data_processed/sub...        40:74       2:3   
17  /Users/julien/temp/neuromod/data_processed/sub...        49:84       2:3   
18  /Users/julien/temp/neuromod/data_processed/sub...        43:77       2:3   
4   /Users/julien/temp/neuromod/data_processed/sub...        19:57       2:3   
14  /Users/julien/temp/neuromod/data_processed/sub...        44:82       2:3   
2   /Users/julien/temp/neuromod/data_processed/sub...        45:81       2:3   
7   /Users/julien/temp/neuromod/data_processed/sub...       89:125       2:3   
5   /Users/julien/temp/neuromod/data_processed/sub...        38:75       2:3   
3   /Users/julien/temp/neuromod/data_processed/sub...        58:95       2:3   

    MEAN(area)  STD(area)  MEAN(angle_AP)  ...  STD(diameter_AP)  \
1    67.680431   1.598728       -4.254822  ...          0.225578   
6    67.511930   1.726861       -6.577358  ...          0.186145   
0    64.109061   3.127582       -4.670983  ...          0.464761   
8    66.455289   4.204379        0.095829  ...          0.684070   
10   73.688109   2.833139       -0.068322  ...          0.406465   
15   73.905494   2.073274       -0.691532  ...          0.368828   
12   69.405673   4.568637       -0.749008  ...          0.543059   
9    59.927681   1.980624       -0.778617  ...          0.334499   
13   60.228814   1.776652       -1.464265  ...          0.247391   
11   60.621684   1.733616       -0.009478  ...          0.358365   
16   59.915665   2.030933       -2.222570  ...          0.296578   
17   59.717857   2.220913        2.572138  ...          0.399145   
18   61.969221   2.026699        6.989458  ...          0.326731   
4    53.010013  11.097434       -1.790824  ...          1.087683   
14   64.717972   4.153035       -3.034680  ...          0.567947   
2    62.953114   1.769023       -0.646246  ...          0.216321   
7    64.823566  18.835219       13.113466  ...          1.159209   
5    62.990802   2.049191       -2.338349  ...          0.298265   
3    63.925810   2.765595       -1.132526  ...          0.248317   

    MEAN(diameter_RL)  STD(diameter_RL)  MEAN(eccentricity)  \
1           10.843164          0.307774            0.680936   
6           10.874612          0.275935            0.690540   
0           10.640776          0.333651            0.690605   
8           11.992443          0.585042            0.794791   
10          12.065046          0.492764            0.756302   
15          12.371408          0.639116            0.780126   
12          12.227376          0.665839            0.796428   
9           10.086060          0.232852            0.658816   
13          10.486967          0.214164            0.716856   
11          10.632869          0.308162            0.726909   
16          10.445562          0.243935            0.716104   
17          10.999128          0.354854            0.775108   
18          10.956739          0.419218            0.753243   
4           10.965275          0.675722            0.822167   
14          11.448594          0.408139            0.769825   
2           11.513113          0.470660            0.792890   
7            9.503113          2.506067            0.576338   
5           11.506661          0.596266            0.792194   
3           11.727604          0.490648            0.803257   

    STD(eccentricity)  MEAN(orientation)  STD(orientation)  MEAN(solidity)  \
1            0.039585           2.149545          1.734302        0.980308   
6            0.031751           2.855729          1.967201        0.977647   
0            0.054994           3.202127          2.184708        0.976971   
8            0.061804           2.234122          1.464966        0.963074   
10           0.053939           2.367144          1.803792        0.966030   
15           0.052688           1.694898          1.187327        0.963111   
12           0.053488           2.145301          1.623586        0.958420   
9            0.049798           2.475063          1.644264        0.972640   
13           0.033921           1.850661          1.538691        0.966100   
11           0.049649           1.681134          1.217510        0.970807   
16           0.038919           2.551453          2.010580        0.972863   
17           0.045832           2.195005          1.555832        0.972639   
18           0.040568           2.095929          1.251544        0.976777   
4            0.059414           4.036279          2.295310        0.952220   
14           0.056204           4.103625          1.847953        0.966696   
2            0.029588           1.260913          1.049494        0.965233   
7            0.152557          22.042768         32.322329        0.968538   
5            0.041279           1.614134          1.158783        0.973527   
3            0.028672           1.754369          1.049329        0.971605   

    STD(solidity)  SUM(length)  
1        0.009615    36.167347  
6        0.008612    32.528253  
0        0.007494    34.565242  
8        0.016533    31.424022  
10       0.009791    32.356730  
15       0.014391    30.534960  
12       0.020529    31.442066  
9        0.009458    28.297791  
13       0.007298    27.236579  
11       0.010769    28.389363  
16       0.010084    28.329492  
17       0.015228    29.056988  
18       0.009427    28.313078  
4        0.027352    33.355815  
14       0.012619    32.529064  
2        0.014776    30.644730  
7        0.032237    10.122137  
5        0.010495    31.364216  
3        0.012450    31.247426  

[19 rows x 24 columns], 'T2w':    Subject Session            Timestamp  \
1        1       1  2021-06-09 23:20:54   
4        1       2  2021-06-09 23:21:02   
0        1       3  2021-06-09 23:20:52   
8        2       1  2021-06-09 23:38:23   
10       2       2  2021-06-09 23:38:28   
15       2       3  2021-06-09 23:48:42   
12       2       4  2021-06-09 23:38:42   
9        3       1  2021-06-09 23:38:25   
13       3       2  2021-06-09 23:38:46   
11       3       3  2021-06-09 23:38:40   
16       3       4  2021-06-09 23:53:25   
17       4       2  2021-06-09 23:53:48   
18       4       3  2021-06-09 23:54:02   
5        5       1  2021-06-09 23:21:05   
14       5       2  2021-06-09 23:38:47   
2        6       1  2021-06-09 23:20:55   
7        6       2  2021-06-09 23:21:12   
6        6       3  2021-06-09 23:21:05   
3        6       4  2021-06-09 23:21:00   

                                          SCT Version  \
1   git-jca/3413-run-batch-session-c41958db922273a...   
4   git-jca/3413-run-batch-session-c41958db922273a...   
0   git-jca/3413-run-batch-session-c41958db922273a...   
8   git-jca/3413-run-batch-session-c41958db922273a...   
10  git-jca/3413-run-batch-session-c41958db922273a...   
15  git-jca/3413-run-batch-session-c41958db922273a...   
12  git-jca/3413-run-batch-session-c41958db922273a...   
9   git-jca/3413-run-batch-session-c41958db922273a...   
13  git-jca/3413-run-batch-session-c41958db922273a...   
11  git-jca/3413-run-batch-session-c41958db922273a...   
16  git-jca/3413-run-batch-session-c41958db922273a...   
17  git-jca/3413-run-batch-session-c41958db922273a...   
18  git-jca/3413-run-batch-session-c41958db922273a...   
5   git-jca/3413-run-batch-session-c41958db922273a...   
14  git-jca/3413-run-batch-session-c41958db922273a...   
2   git-jca/3413-run-batch-session-c41958db922273a...   
7   git-jca/3413-run-batch-session-c41958db922273a...   
6   git-jca/3413-run-batch-session-c41958db922273a...   
3   git-jca/3413-run-batch-session-c41958db922273a...   

                                             Filename Slice (I->S) VertLevel  \
1   /Users/julien/temp/neuromod/data_processed/sub...      160:201       2:3   
4   /Users/julien/temp/neuromod/data_processed/sub...      162:203       2:3   
0   /Users/julien/temp/neuromod/data_processed/sub...      161:203       2:3   
8   /Users/julien/temp/neuromod/data_processed/sub...      157:193       2:3   
10  /Users/julien/temp/neuromod/data_processed/sub...      156:191       2:3   
15  /Users/julien/temp/neuromod/data_processed/sub...      159:193       2:3   
12  /Users/julien/temp/neuromod/data_processed/sub...      160:193       2:3   
9   /Users/julien/temp/neuromod/data_processed/sub...      141:177       2:3   
13  /Users/julien/temp/neuromod/data_processed/sub...      162:198       2:3   
11  /Users/julien/temp/neuromod/data_processed/sub...      161:196       2:3   
16  /Users/julien/temp/neuromod/data_processed/sub...      158:194       2:3   
17  /Users/julien/temp/neuromod/data_processed/sub...      164:200       2:3   
18  /Users/julien/temp/neuromod/data_processed/sub...      164:199       2:3   
5   /Users/julien/temp/neuromod/data_processed/sub...      159:196       2:3   
14  /Users/julien/temp/neuromod/data_processed/sub...      154:191       2:3   
2   /Users/julien/temp/neuromod/data_processed/sub...      158:194       2:3   
7   /Users/julien/temp/neuromod/data_processed/sub...      164:200       2:3   
6   /Users/julien/temp/neuromod/data_processed/sub...      166:201       2:3   
3   /Users/julien/temp/neuromod/data_processed/sub...      167:203       2:3   

    MEAN(area)  STD(area)  MEAN(angle_AP)  ...  STD(diameter_AP)  \
1    80.312877   1.602798       -3.958454  ...          0.148831   
4    80.768423   1.967870       -5.074403  ...          0.180384   
0    80.774162   3.246713       -3.760068  ...          0.174290   
8    92.724125   7.198446       -0.533592  ...          0.500942   
10   94.587712   7.628431       -0.855157  ...          0.571808   
15   92.666900   8.162162       -0.596256  ...          0.609800   
12   93.571468   6.715923       -1.310382  ...          0.499746   
9    73.617773   1.283275       -0.176559  ...          0.162039   
13   72.980170   1.733563       -0.169089  ...          0.218192   
11   70.593648   1.455799       -0.991364  ...          0.267249   
16   71.268228   1.688296        0.149827  ...          0.272076   
17   74.732375   0.995570       -0.057076  ...          0.173023   
18   75.005645   0.909686        4.142686  ...          0.251494   
5    70.779953   4.773098       -1.899860  ...          0.773255   
14   74.857807   2.759146       -2.745917  ...          0.388765   
2    72.958267   2.394267       -0.230000  ...          0.206093   
7    73.129881   1.990473       -0.959923  ...          0.223915   
6    73.894805   2.227882        0.547178  ...          0.174199   
3    72.129244   2.513562       -2.145414  ...          0.180008   

    MEAN(diameter_RL)  STD(diameter_RL)  MEAN(eccentricity)  \
1           11.899994          0.348936            0.689786   
4           11.935064          0.352203            0.692630   
0           11.942165          0.386189            0.692055   
8           13.469831          0.903365            0.749762   
10          13.618790          0.856929            0.751709   
15          13.567128          0.933170            0.758917   
12          13.510144          0.754180            0.750687   
9           11.618506          0.249626            0.719638   
13          11.669006          0.227977            0.728585   
11          11.246244          0.328627            0.702012   
16          11.275181          0.260300            0.698106   
17          12.063074          0.345358            0.754853   
18          11.967497          0.381923            0.743363   
5           12.190368          0.565430            0.779750   
14          12.401970          0.406430            0.775455   
2           12.298752          0.455764            0.786437   
7           12.384761          0.445033            0.792261   
6           12.449794          0.470167            0.792112   
3           12.327045          0.417297            0.794967   

    STD(eccentricity)  MEAN(orientation)  STD(orientation)  MEAN(solidity)  \
1            0.032309           3.342223          1.895299        0.973535   
4            0.031759           2.725679          1.980338        0.974296   
0            0.028034           4.826952          2.124976        0.973148   
8            0.061652           3.007144          1.340842        0.970252   
10           0.060540           2.065212          1.229055        0.970512   
15           0.066758           1.366771          1.115320        0.969417   
12           0.055164           1.432686          1.105488        0.970806   
9            0.026723           1.350991          0.866047        0.970433   
13           0.027002           1.021736          0.860224        0.971586   
11           0.046127           1.260142          1.145153        0.970805   
16           0.041606           1.752418          1.216747        0.975077   
17           0.027804           2.550164          1.247343        0.967420   
18           0.040588           1.571435          1.604254        0.972454   
5            0.071128           3.074997          1.954591        0.956469   
14           0.041603           2.156050          1.223840        0.966862   
2            0.025628           0.972269          0.813403        0.972373   
7            0.026887           1.640786          1.149530        0.970194   
6            0.023507           1.604021          1.084022        0.967781   
3            0.019853           1.783156          0.920410        0.969491   

    STD(solidity)  SUM(length)  
1        0.009511    33.716889  
4        0.007769    33.951292  
0        0.006615    34.526392  
8        0.010245    31.142010  
10       0.010239    30.640014  
15       0.010025    29.350071  
12       0.009661    28.757132  
9        0.008960    29.966024  
13       0.007557    29.619905  
11       0.008657    29.249095  
16       0.009043    30.022830  
17       0.011174    29.705806  
18       0.008886    28.928858  
5        0.019386    31.359579  
14       0.013124    31.380837  
2        0.010028    30.494727  
7        0.011049    30.874411  
6        0.010371    29.962644  
3        0.009872    30.558270  

[19 rows x 24 columns], 'GMT2w':    Subject Session            Timestamp  \
0        1       1  2021-06-09 23:27:57   
5        1       2  2021-06-09 23:28:30   
1        1       3  2021-06-09 23:28:01   
8        2       1  2021-06-09 23:44:35   
9        2       2  2021-06-09 23:45:01   
14       2       3  2021-06-09 23:53:03   
11       2       4  2021-06-09 23:45:18   
10       3       1  2021-06-09 23:45:12   
13       3       2  2021-06-09 23:45:45   
12       3       3  2021-06-09 23:45:36   
15       3       4  2021-06-09 23:57:39   
16       4       2  2021-06-09 23:58:05   
17       4       3  2021-06-09 23:58:21   
4        5       1  2021-06-09 23:28:25   
2        6       1  2021-06-09 23:28:13   
7        6       2  2021-06-09 23:28:34   
6        6       3  2021-06-09 23:28:31   
3        6       4  2021-06-09 23:28:22   

                                          SCT Version  \
0   git-jca/3413-run-batch-session-c41958db922273a...   
5   git-jca/3413-run-batch-session-c41958db922273a...   
1   git-jca/3413-run-batch-session-c41958db922273a...   
8   git-jca/3413-run-batch-session-c41958db922273a...   
9   git-jca/3413-run-batch-session-c41958db922273a...   
14  git-jca/3413-run-batch-session-c41958db922273a...   
11  git-jca/3413-run-batch-session-c41958db922273a...   
10  git-jca/3413-run-batch-session-c41958db922273a...   
13  git-jca/3413-run-batch-session-c41958db922273a...   
12  git-jca/3413-run-batch-session-c41958db922273a...   
15  git-jca/3413-run-batch-session-c41958db922273a...   
16  git-jca/3413-run-batch-session-c41958db922273a...   
17  git-jca/3413-run-batch-session-c41958db922273a...   
4   git-jca/3413-run-batch-session-c41958db922273a...   
2   git-jca/3413-run-batch-session-c41958db922273a...   
7   git-jca/3413-run-batch-session-c41958db922273a...   
6   git-jca/3413-run-batch-session-c41958db922273a...   
3   git-jca/3413-run-batch-session-c41958db922273a...   

                                             Filename Slice (I->S) VertLevel  \
0   /Users/julien/temp/neuromod/data_processed/sub...          2:9       3:4   
5   /Users/julien/temp/neuromod/data_processed/sub...         4:10       3:4   
1   /Users/julien/temp/neuromod/data_processed/sub...         4:10       3:4   
8   /Users/julien/temp/neuromod/data_processed/sub...         4:10       3:4   
9   /Users/julien/temp/neuromod/data_processed/sub...          3:9       3:4   
14  /Users/julien/temp/neuromod/data_processed/sub...         4:10       3:4   
11  /Users/julien/temp/neuromod/data_processed/sub...          3:9       3:4   
10  /Users/julien/temp/neuromod/data_processed/sub...          4:9       3:4   
13  /Users/julien/temp/neuromod/data_processed/sub...         5:10       3:4   
12  /Users/julien/temp/neuromod/data_processed/sub...         5:10       3:4   
15  /Users/julien/temp/neuromod/data_processed/sub...          4:9       3:4   
16  /Users/julien/temp/neuromod/data_processed/sub...          4:9       3:4   
17  /Users/julien/temp/neuromod/data_processed/sub...         5:10       3:4   
4   /Users/julien/temp/neuromod/data_processed/sub...         4:10       3:4   
2   /Users/julien/temp/neuromod/data_processed/sub...         4:10       3:4   
7   /Users/julien/temp/neuromod/data_processed/sub...         4:10       3:4   
6   /Users/julien/temp/neuromod/data_processed/sub...         4:10       3:4   
3   /Users/julien/temp/neuromod/data_processed/sub...         4:10       3:4   

    MEAN(area)  STD(area)  MEAN(angle_AP)  ...  STD(diameter_AP)  \
0    15.781250   1.371800             0.0  ...          0.283857   
5    15.928571   2.034147             0.0  ...          0.312646   
1    17.000000   1.752549             0.0  ...          0.437912   
8    19.821429   1.360897             0.0  ...          0.417456   
9    20.000000   1.077365             0.0  ...          0.342271   
14   19.214286   1.605952             0.0  ...          0.487494   
11   20.464286   1.397885             0.0  ...          0.322935   
10   18.208333   1.933351             0.0  ...          0.218711   
13   17.333333   1.624466             0.0  ...          0.157746   
12   16.625000   2.452677             0.0  ...          0.185884   
15   16.958333   1.758412             0.0  ...          0.238859   
16   17.041667   1.417279             0.0  ...          0.193646   
17   17.333332   1.455354             0.0  ...          0.309761   
4    16.214286   1.848883             0.0  ...          0.490131   
2    16.642857   3.600241             0.0  ...          0.556421   
7    17.392857   2.182958             0.0  ...          0.433186   
6    16.321428   2.020936             0.0  ...          0.451914   
3    16.535714   2.707228             0.0  ...          0.719459   

    MEAN(diameter_RL)  STD(diameter_RL)  MEAN(eccentricity)  \
0            9.157261          0.632701            0.760794   
5            8.912826          0.518961            0.755229   
1            9.105736          0.577677            0.742294   
8           11.544729          0.413976            0.882456   
9           11.842302          0.579720            0.879404   
14          11.589557          0.509289            0.880191   
11          11.748837          0.339294            0.880092   
10           9.713868          0.912814            0.809431   
13           9.552361          0.850671            0.803472   
12           9.541168          0.905707            0.803929   
15           9.512255          0.787789            0.809049   
16           9.258316          0.625445            0.800148   
17           9.310330          0.966440            0.792127   
4            9.916864          0.663039            0.848935   
2           10.865812          0.972017            0.875254   
7           11.029238          0.908874            0.877292   
6           10.450533          0.889613            0.879650   
3           10.447901          0.631897            0.896789   

    STD(eccentricity)  MEAN(orientation)  STD(orientation)  MEAN(solidity)  \
0            0.065413           9.239814          4.915181        0.398420   
5            0.050143           7.501914          6.651370        0.402462   
1            0.076859           8.999431          5.426012        0.412780   
8            0.015014           2.491855          1.419888        0.400532   
9            0.021123           2.516891          2.068491        0.380244   
14           0.021772           3.755927          2.144876        0.392944   
11           0.017030           1.848681          1.410178        0.390731   
10           0.046939           2.111163          1.302024        0.441700   
13           0.048638           3.743699          2.736344        0.431054   
12           0.050888           3.033851          3.309783        0.423130   
15           0.050811           2.475007          0.736044        0.427416   
16           0.040699           3.309946          1.876603        0.438293   
17           0.067271           5.133278          3.005962        0.452724   
4            0.047865           3.056269          2.330227        0.420649   
2            0.043939           1.272704          0.738812        0.392086   
7            0.037499           1.582275          1.103783        0.406786   
6            0.036167           1.582814          1.583200        0.423449   
3            0.037479           3.565542          1.894078        0.461639   

    STD(solidity)  SUM(length)  
0        0.017171    40.000000  
5        0.017327    34.999983  
1        0.019752    35.000010  
8        0.022981    35.000033  
9        0.013678    34.999980  
14       0.018671    35.000000  
11       0.011656    35.000033  
10       0.014227    29.999989  
13       0.016436    30.000037  
12       0.022843    29.999986  
15       0.020870    29.999991  
16       0.010648    30.000011  
17       0.024747    30.000011  
4        0.020092    34.999977  
2        0.054614    34.999983  
7        0.024975    34.999990  
6        0.020716    35.000017  
3        0.037115    35.000003  

[18 rows x 24 columns]}

Gray matter CSA#

fig_spine = Plot(dataset, plot_name = 'spine-2')
fig_spine.title = 'Spinal cord gray matter CSA'
# If you're running this notebook in a Jupyter Notebook (eg, on MyBinder), change 'jupyter-book' to 'notebook'
fig_spine.display('jupyter-book', tissue = 'GM')
{'T1w':    Subject Session            Timestamp  \
1        1       1  2021-06-09 23:24:10   
6        1       2  2021-06-09 23:24:19   
0        1       3  2021-06-09 23:24:08   
8        2       1  2021-06-09 23:41:15   
10       2       2  2021-06-09 23:41:24   
15       2       3  2021-06-09 23:50:43   
12       2       4  2021-06-09 23:41:39   
9        3       1  2021-06-09 23:41:20   
13       3       2  2021-06-09 23:41:42   
11       3       3  2021-06-09 23:41:39   
16       3       4  2021-06-09 23:55:17   
17       4       2  2021-06-09 23:55:38   
18       4       3  2021-06-09 23:55:53   
4        5       1  2021-06-09 23:24:18   
14       5       2  2021-06-09 23:41:45   
2        6       1  2021-06-09 23:24:11   
7        6       2  2021-06-09 23:24:21   
5        6       3  2021-06-09 23:24:19   
3        6       4  2021-06-09 23:24:12   

                                          SCT Version  \
1   git-jca/3413-run-batch-session-c41958db922273a...   
6   git-jca/3413-run-batch-session-c41958db922273a...   
0   git-jca/3413-run-batch-session-c41958db922273a...   
8   git-jca/3413-run-batch-session-c41958db922273a...   
10  git-jca/3413-run-batch-session-c41958db922273a...   
15  git-jca/3413-run-batch-session-c41958db922273a...   
12  git-jca/3413-run-batch-session-c41958db922273a...   
9   git-jca/3413-run-batch-session-c41958db922273a...   
13  git-jca/3413-run-batch-session-c41958db922273a...   
11  git-jca/3413-run-batch-session-c41958db922273a...   
16  git-jca/3413-run-batch-session-c41958db922273a...   
17  git-jca/3413-run-batch-session-c41958db922273a...   
18  git-jca/3413-run-batch-session-c41958db922273a...   
4   git-jca/3413-run-batch-session-c41958db922273a...   
14  git-jca/3413-run-batch-session-c41958db922273a...   
2   git-jca/3413-run-batch-session-c41958db922273a...   
7   git-jca/3413-run-batch-session-c41958db922273a...   
5   git-jca/3413-run-batch-session-c41958db922273a...   
3   git-jca/3413-run-batch-session-c41958db922273a...   

                                             Filename Slice (I->S) VertLevel  \
1   /Users/julien/temp/neuromod/data_processed/sub...        31:75       2:3   
6   /Users/julien/temp/neuromod/data_processed/sub...        47:86       2:3   
0   /Users/julien/temp/neuromod/data_processed/sub...        51:93       2:3   
8   /Users/julien/temp/neuromod/data_processed/sub...         1:38       2:3   
10  /Users/julien/temp/neuromod/data_processed/sub...        12:50       2:3   
15  /Users/julien/temp/neuromod/data_processed/sub...         3:39       2:3   
12  /Users/julien/temp/neuromod/data_processed/sub...         9:46       2:3   
9   /Users/julien/temp/neuromod/data_processed/sub...        51:85       2:3   
13  /Users/julien/temp/neuromod/data_processed/sub...        33:66       2:3   
11  /Users/julien/temp/neuromod/data_processed/sub...        43:77       2:3   
16  /Users/julien/temp/neuromod/data_processed/sub...        40:74       2:3   
17  /Users/julien/temp/neuromod/data_processed/sub...        49:84       2:3   
18  /Users/julien/temp/neuromod/data_processed/sub...        43:77       2:3   
4   /Users/julien/temp/neuromod/data_processed/sub...        19:57       2:3   
14  /Users/julien/temp/neuromod/data_processed/sub...        44:82       2:3   
2   /Users/julien/temp/neuromod/data_processed/sub...        45:81       2:3   
7   /Users/julien/temp/neuromod/data_processed/sub...       89:125       2:3   
5   /Users/julien/temp/neuromod/data_processed/sub...        38:75       2:3   
3   /Users/julien/temp/neuromod/data_processed/sub...        58:95       2:3   

    MEAN(area)  STD(area)  MEAN(angle_AP)  ...  STD(diameter_AP)  \
1    67.680431   1.598728       -4.254822  ...          0.225578   
6    67.511930   1.726861       -6.577358  ...          0.186145   
0    64.109061   3.127582       -4.670983  ...          0.464761   
8    66.455289   4.204379        0.095829  ...          0.684070   
10   73.688109   2.833139       -0.068322  ...          0.406465   
15   73.905494   2.073274       -0.691532  ...          0.368828   
12   69.405673   4.568637       -0.749008  ...          0.543059   
9    59.927681   1.980624       -0.778617  ...          0.334499   
13   60.228814   1.776652       -1.464265  ...          0.247391   
11   60.621684   1.733616       -0.009478  ...          0.358365   
16   59.915665   2.030933       -2.222570  ...          0.296578   
17   59.717857   2.220913        2.572138  ...          0.399145   
18   61.969221   2.026699        6.989458  ...          0.326731   
4    53.010013  11.097434       -1.790824  ...          1.087683   
14   64.717972   4.153035       -3.034680  ...          0.567947   
2    62.953114   1.769023       -0.646246  ...          0.216321   
7    64.823566  18.835219       13.113466  ...          1.159209   
5    62.990802   2.049191       -2.338349  ...          0.298265   
3    63.925810   2.765595       -1.132526  ...          0.248317   

    MEAN(diameter_RL)  STD(diameter_RL)  MEAN(eccentricity)  \
1           10.843164          0.307774            0.680936   
6           10.874612          0.275935            0.690540   
0           10.640776          0.333651            0.690605   
8           11.992443          0.585042            0.794791   
10          12.065046          0.492764            0.756302   
15          12.371408          0.639116            0.780126   
12          12.227376          0.665839            0.796428   
9           10.086060          0.232852            0.658816   
13          10.486967          0.214164            0.716856   
11          10.632869          0.308162            0.726909   
16          10.445562          0.243935            0.716104   
17          10.999128          0.354854            0.775108   
18          10.956739          0.419218            0.753243   
4           10.965275          0.675722            0.822167   
14          11.448594          0.408139            0.769825   
2           11.513113          0.470660            0.792890   
7            9.503113          2.506067            0.576338   
5           11.506661          0.596266            0.792194   
3           11.727604          0.490648            0.803257   

    STD(eccentricity)  MEAN(orientation)  STD(orientation)  MEAN(solidity)  \
1            0.039585           2.149545          1.734302        0.980308   
6            0.031751           2.855729          1.967201        0.977647   
0            0.054994           3.202127          2.184708        0.976971   
8            0.061804           2.234122          1.464966        0.963074   
10           0.053939           2.367144          1.803792        0.966030   
15           0.052688           1.694898          1.187327        0.963111   
12           0.053488           2.145301          1.623586        0.958420   
9            0.049798           2.475063          1.644264        0.972640   
13           0.033921           1.850661          1.538691        0.966100   
11           0.049649           1.681134          1.217510        0.970807   
16           0.038919           2.551453          2.010580        0.972863   
17           0.045832           2.195005          1.555832        0.972639   
18           0.040568           2.095929          1.251544        0.976777   
4            0.059414           4.036279          2.295310        0.952220   
14           0.056204           4.103625          1.847953        0.966696   
2            0.029588           1.260913          1.049494        0.965233   
7            0.152557          22.042768         32.322329        0.968538   
5            0.041279           1.614134          1.158783        0.973527   
3            0.028672           1.754369          1.049329        0.971605   

    STD(solidity)  SUM(length)  
1        0.009615    36.167347  
6        0.008612    32.528253  
0        0.007494    34.565242  
8        0.016533    31.424022  
10       0.009791    32.356730  
15       0.014391    30.534960  
12       0.020529    31.442066  
9        0.009458    28.297791  
13       0.007298    27.236579  
11       0.010769    28.389363  
16       0.010084    28.329492  
17       0.015228    29.056988  
18       0.009427    28.313078  
4        0.027352    33.355815  
14       0.012619    32.529064  
2        0.014776    30.644730  
7        0.032237    10.122137  
5        0.010495    31.364216  
3        0.012450    31.247426  

[19 rows x 24 columns], 'T2w':    Subject Session            Timestamp  \
1        1       1  2021-06-09 23:20:54   
4        1       2  2021-06-09 23:21:02   
0        1       3  2021-06-09 23:20:52   
8        2       1  2021-06-09 23:38:23   
10       2       2  2021-06-09 23:38:28   
15       2       3  2021-06-09 23:48:42   
12       2       4  2021-06-09 23:38:42   
9        3       1  2021-06-09 23:38:25   
13       3       2  2021-06-09 23:38:46   
11       3       3  2021-06-09 23:38:40   
16       3       4  2021-06-09 23:53:25   
17       4       2  2021-06-09 23:53:48   
18       4       3  2021-06-09 23:54:02   
5        5       1  2021-06-09 23:21:05   
14       5       2  2021-06-09 23:38:47   
2        6       1  2021-06-09 23:20:55   
7        6       2  2021-06-09 23:21:12   
6        6       3  2021-06-09 23:21:05   
3        6       4  2021-06-09 23:21:00   

                                          SCT Version  \
1   git-jca/3413-run-batch-session-c41958db922273a...   
4   git-jca/3413-run-batch-session-c41958db922273a...   
0   git-jca/3413-run-batch-session-c41958db922273a...   
8   git-jca/3413-run-batch-session-c41958db922273a...   
10  git-jca/3413-run-batch-session-c41958db922273a...   
15  git-jca/3413-run-batch-session-c41958db922273a...   
12  git-jca/3413-run-batch-session-c41958db922273a...   
9   git-jca/3413-run-batch-session-c41958db922273a...   
13  git-jca/3413-run-batch-session-c41958db922273a...   
11  git-jca/3413-run-batch-session-c41958db922273a...   
16  git-jca/3413-run-batch-session-c41958db922273a...   
17  git-jca/3413-run-batch-session-c41958db922273a...   
18  git-jca/3413-run-batch-session-c41958db922273a...   
5   git-jca/3413-run-batch-session-c41958db922273a...   
14  git-jca/3413-run-batch-session-c41958db922273a...   
2   git-jca/3413-run-batch-session-c41958db922273a...   
7   git-jca/3413-run-batch-session-c41958db922273a...   
6   git-jca/3413-run-batch-session-c41958db922273a...   
3   git-jca/3413-run-batch-session-c41958db922273a...   

                                             Filename Slice (I->S) VertLevel  \
1   /Users/julien/temp/neuromod/data_processed/sub...      160:201       2:3   
4   /Users/julien/temp/neuromod/data_processed/sub...      162:203       2:3   
0   /Users/julien/temp/neuromod/data_processed/sub...      161:203       2:3   
8   /Users/julien/temp/neuromod/data_processed/sub...      157:193       2:3   
10  /Users/julien/temp/neuromod/data_processed/sub...      156:191       2:3   
15  /Users/julien/temp/neuromod/data_processed/sub...      159:193       2:3   
12  /Users/julien/temp/neuromod/data_processed/sub...      160:193       2:3   
9   /Users/julien/temp/neuromod/data_processed/sub...      141:177       2:3   
13  /Users/julien/temp/neuromod/data_processed/sub...      162:198       2:3   
11  /Users/julien/temp/neuromod/data_processed/sub...      161:196       2:3   
16  /Users/julien/temp/neuromod/data_processed/sub...      158:194       2:3   
17  /Users/julien/temp/neuromod/data_processed/sub...      164:200       2:3   
18  /Users/julien/temp/neuromod/data_processed/sub...      164:199       2:3   
5   /Users/julien/temp/neuromod/data_processed/sub...      159:196       2:3   
14  /Users/julien/temp/neuromod/data_processed/sub...      154:191       2:3   
2   /Users/julien/temp/neuromod/data_processed/sub...      158:194       2:3   
7   /Users/julien/temp/neuromod/data_processed/sub...      164:200       2:3   
6   /Users/julien/temp/neuromod/data_processed/sub...      166:201       2:3   
3   /Users/julien/temp/neuromod/data_processed/sub...      167:203       2:3   

    MEAN(area)  STD(area)  MEAN(angle_AP)  ...  STD(diameter_AP)  \
1    80.312877   1.602798       -3.958454  ...          0.148831   
4    80.768423   1.967870       -5.074403  ...          0.180384   
0    80.774162   3.246713       -3.760068  ...          0.174290   
8    92.724125   7.198446       -0.533592  ...          0.500942   
10   94.587712   7.628431       -0.855157  ...          0.571808   
15   92.666900   8.162162       -0.596256  ...          0.609800   
12   93.571468   6.715923       -1.310382  ...          0.499746   
9    73.617773   1.283275       -0.176559  ...          0.162039   
13   72.980170   1.733563       -0.169089  ...          0.218192   
11   70.593648   1.455799       -0.991364  ...          0.267249   
16   71.268228   1.688296        0.149827  ...          0.272076   
17   74.732375   0.995570       -0.057076  ...          0.173023   
18   75.005645   0.909686        4.142686  ...          0.251494   
5    70.779953   4.773098       -1.899860  ...          0.773255   
14   74.857807   2.759146       -2.745917  ...          0.388765   
2    72.958267   2.394267       -0.230000  ...          0.206093   
7    73.129881   1.990473       -0.959923  ...          0.223915   
6    73.894805   2.227882        0.547178  ...          0.174199   
3    72.129244   2.513562       -2.145414  ...          0.180008   

    MEAN(diameter_RL)  STD(diameter_RL)  MEAN(eccentricity)  \
1           11.899994          0.348936            0.689786   
4           11.935064          0.352203            0.692630   
0           11.942165          0.386189            0.692055   
8           13.469831          0.903365            0.749762   
10          13.618790          0.856929            0.751709   
15          13.567128          0.933170            0.758917   
12          13.510144          0.754180            0.750687   
9           11.618506          0.249626            0.719638   
13          11.669006          0.227977            0.728585   
11          11.246244          0.328627            0.702012   
16          11.275181          0.260300            0.698106   
17          12.063074          0.345358            0.754853   
18          11.967497          0.381923            0.743363   
5           12.190368          0.565430            0.779750   
14          12.401970          0.406430            0.775455   
2           12.298752          0.455764            0.786437   
7           12.384761          0.445033            0.792261   
6           12.449794          0.470167            0.792112   
3           12.327045          0.417297            0.794967   

    STD(eccentricity)  MEAN(orientation)  STD(orientation)  MEAN(solidity)  \
1            0.032309           3.342223          1.895299        0.973535   
4            0.031759           2.725679          1.980338        0.974296   
0            0.028034           4.826952          2.124976        0.973148   
8            0.061652           3.007144          1.340842        0.970252   
10           0.060540           2.065212          1.229055        0.970512   
15           0.066758           1.366771          1.115320        0.969417   
12           0.055164           1.432686          1.105488        0.970806   
9            0.026723           1.350991          0.866047        0.970433   
13           0.027002           1.021736          0.860224        0.971586   
11           0.046127           1.260142          1.145153        0.970805   
16           0.041606           1.752418          1.216747        0.975077   
17           0.027804           2.550164          1.247343        0.967420   
18           0.040588           1.571435          1.604254        0.972454   
5            0.071128           3.074997          1.954591        0.956469   
14           0.041603           2.156050          1.223840        0.966862   
2            0.025628           0.972269          0.813403        0.972373   
7            0.026887           1.640786          1.149530        0.970194   
6            0.023507           1.604021          1.084022        0.967781   
3            0.019853           1.783156          0.920410        0.969491   

    STD(solidity)  SUM(length)  
1        0.009511    33.716889  
4        0.007769    33.951292  
0        0.006615    34.526392  
8        0.010245    31.142010  
10       0.010239    30.640014  
15       0.010025    29.350071  
12       0.009661    28.757132  
9        0.008960    29.966024  
13       0.007557    29.619905  
11       0.008657    29.249095  
16       0.009043    30.022830  
17       0.011174    29.705806  
18       0.008886    28.928858  
5        0.019386    31.359579  
14       0.013124    31.380837  
2        0.010028    30.494727  
7        0.011049    30.874411  
6        0.010371    29.962644  
3        0.009872    30.558270  

[19 rows x 24 columns], 'GMT2w':    Subject Session            Timestamp  \
0        1       1  2021-06-09 23:27:57   
5        1       2  2021-06-09 23:28:30   
1        1       3  2021-06-09 23:28:01   
8        2       1  2021-06-09 23:44:35   
9        2       2  2021-06-09 23:45:01   
14       2       3  2021-06-09 23:53:03   
11       2       4  2021-06-09 23:45:18   
10       3       1  2021-06-09 23:45:12   
13       3       2  2021-06-09 23:45:45   
12       3       3  2021-06-09 23:45:36   
15       3       4  2021-06-09 23:57:39   
16       4       2  2021-06-09 23:58:05   
17       4       3  2021-06-09 23:58:21   
4        5       1  2021-06-09 23:28:25   
2        6       1  2021-06-09 23:28:13   
7        6       2  2021-06-09 23:28:34   
6        6       3  2021-06-09 23:28:31   
3        6       4  2021-06-09 23:28:22   

                                          SCT Version  \
0   git-jca/3413-run-batch-session-c41958db922273a...   
5   git-jca/3413-run-batch-session-c41958db922273a...   
1   git-jca/3413-run-batch-session-c41958db922273a...   
8   git-jca/3413-run-batch-session-c41958db922273a...   
9   git-jca/3413-run-batch-session-c41958db922273a...   
14  git-jca/3413-run-batch-session-c41958db922273a...   
11  git-jca/3413-run-batch-session-c41958db922273a...   
10  git-jca/3413-run-batch-session-c41958db922273a...   
13  git-jca/3413-run-batch-session-c41958db922273a...   
12  git-jca/3413-run-batch-session-c41958db922273a...   
15  git-jca/3413-run-batch-session-c41958db922273a...   
16  git-jca/3413-run-batch-session-c41958db922273a...   
17  git-jca/3413-run-batch-session-c41958db922273a...   
4   git-jca/3413-run-batch-session-c41958db922273a...   
2   git-jca/3413-run-batch-session-c41958db922273a...   
7   git-jca/3413-run-batch-session-c41958db922273a...   
6   git-jca/3413-run-batch-session-c41958db922273a...   
3   git-jca/3413-run-batch-session-c41958db922273a...   

                                             Filename Slice (I->S) VertLevel  \
0   /Users/julien/temp/neuromod/data_processed/sub...          2:9       3:4   
5   /Users/julien/temp/neuromod/data_processed/sub...         4:10       3:4   
1   /Users/julien/temp/neuromod/data_processed/sub...         4:10       3:4   
8   /Users/julien/temp/neuromod/data_processed/sub...         4:10       3:4   
9   /Users/julien/temp/neuromod/data_processed/sub...          3:9       3:4   
14  /Users/julien/temp/neuromod/data_processed/sub...         4:10       3:4   
11  /Users/julien/temp/neuromod/data_processed/sub...          3:9       3:4   
10  /Users/julien/temp/neuromod/data_processed/sub...          4:9       3:4   
13  /Users/julien/temp/neuromod/data_processed/sub...         5:10       3:4   
12  /Users/julien/temp/neuromod/data_processed/sub...         5:10       3:4   
15  /Users/julien/temp/neuromod/data_processed/sub...          4:9       3:4   
16  /Users/julien/temp/neuromod/data_processed/sub...          4:9       3:4   
17  /Users/julien/temp/neuromod/data_processed/sub...         5:10       3:4   
4   /Users/julien/temp/neuromod/data_processed/sub...         4:10       3:4   
2   /Users/julien/temp/neuromod/data_processed/sub...         4:10       3:4   
7   /Users/julien/temp/neuromod/data_processed/sub...         4:10       3:4   
6   /Users/julien/temp/neuromod/data_processed/sub...         4:10       3:4   
3   /Users/julien/temp/neuromod/data_processed/sub...         4:10       3:4   

    MEAN(area)  STD(area)  MEAN(angle_AP)  ...  STD(diameter_AP)  \
0    15.781250   1.371800             0.0  ...          0.283857   
5    15.928571   2.034147             0.0  ...          0.312646   
1    17.000000   1.752549             0.0  ...          0.437912   
8    19.821429   1.360897             0.0  ...          0.417456   
9    20.000000   1.077365             0.0  ...          0.342271   
14   19.214286   1.605952             0.0  ...          0.487494   
11   20.464286   1.397885             0.0  ...          0.322935   
10   18.208333   1.933351             0.0  ...          0.218711   
13   17.333333   1.624466             0.0  ...          0.157746   
12   16.625000   2.452677             0.0  ...          0.185884   
15   16.958333   1.758412             0.0  ...          0.238859   
16   17.041667   1.417279             0.0  ...          0.193646   
17   17.333332   1.455354             0.0  ...          0.309761   
4    16.214286   1.848883             0.0  ...          0.490131   
2    16.642857   3.600241             0.0  ...          0.556421   
7    17.392857   2.182958             0.0  ...          0.433186   
6    16.321428   2.020936             0.0  ...          0.451914   
3    16.535714   2.707228             0.0  ...          0.719459   

    MEAN(diameter_RL)  STD(diameter_RL)  MEAN(eccentricity)  \
0            9.157261          0.632701            0.760794   
5            8.912826          0.518961            0.755229   
1            9.105736          0.577677            0.742294   
8           11.544729          0.413976            0.882456   
9           11.842302          0.579720            0.879404   
14          11.589557          0.509289            0.880191   
11          11.748837          0.339294            0.880092   
10           9.713868          0.912814            0.809431   
13           9.552361          0.850671            0.803472   
12           9.541168          0.905707            0.803929   
15           9.512255          0.787789            0.809049   
16           9.258316          0.625445            0.800148   
17           9.310330          0.966440            0.792127   
4            9.916864          0.663039            0.848935   
2           10.865812          0.972017            0.875254   
7           11.029238          0.908874            0.877292   
6           10.450533          0.889613            0.879650   
3           10.447901          0.631897            0.896789   

    STD(eccentricity)  MEAN(orientation)  STD(orientation)  MEAN(solidity)  \
0            0.065413           9.239814          4.915181        0.398420   
5            0.050143           7.501914          6.651370        0.402462   
1            0.076859           8.999431          5.426012        0.412780   
8            0.015014           2.491855          1.419888        0.400532   
9            0.021123           2.516891          2.068491        0.380244   
14           0.021772           3.755927          2.144876        0.392944   
11           0.017030           1.848681          1.410178        0.390731   
10           0.046939           2.111163          1.302024        0.441700   
13           0.048638           3.743699          2.736344        0.431054   
12           0.050888           3.033851          3.309783        0.423130   
15           0.050811           2.475007          0.736044        0.427416   
16           0.040699           3.309946          1.876603        0.438293   
17           0.067271           5.133278          3.005962        0.452724   
4            0.047865           3.056269          2.330227        0.420649   
2            0.043939           1.272704          0.738812        0.392086   
7            0.037499           1.582275          1.103783        0.406786   
6            0.036167           1.582814          1.583200        0.423449   
3            0.037479           3.565542          1.894078        0.461639   

    STD(solidity)  SUM(length)  
0        0.017171    40.000000  
5        0.017327    34.999983  
1        0.019752    35.000010  
8        0.022981    35.000033  
9        0.013678    34.999980  
14       0.018671    35.000000  
11       0.011656    35.000033  
10       0.014227    29.999989  
13       0.016436    30.000037  
12       0.022843    29.999986  
15       0.020870    29.999991  
16       0.010648    30.000011  
17       0.024747    30.000011  
4        0.020092    34.999977  
2        0.054614    34.999983  
7        0.024975    34.999990  
6        0.020716    35.000017  
3        0.037115    35.000003  

[18 rows x 24 columns]}

White matter qMRI#

data_type = 'qmri'
release_version = 'latest'

dataset = Data(data_type)
dataset.download(release_version)
Archive:  spinalcord_results.zip
  inflating: data/qmri/DWI_RD.csv    
  inflating: data/qmri/DWI_FA.csv    
  inflating: data/qmri/csa-SC_T2w.csv  
  inflating: data/qmri/DWI_MD.csv    
  inflating: data/qmri/MTR.csv       
  inflating: data/qmri/MTsat.csv     
  inflating: data/qmri/csa-GM_T2s.csv  
  inflating: data/qmri/csa-SC_T1w.csv  
  inflating: data/qmri/._csa-SC_T1w.csv  
  inflating: data/qmri/T1.csv        
--2022-06-14 00:05:37--  https://github.com/courtois-neuromod/anat-processing/releases/download//r20210610/spinalcord_results.zip
Resolving github.com (github.com)... 140.82.114.4
Connecting to github.com (github.com)|140.82.114.4|:443... connected.
HTTP request sent, awaiting response... 302 Found
Location: https://objects.githubusercontent.com/github-production-release-asset-2e65be/333825187/9e444c00-c9e2-11eb-880c-f9aa2a43f100?X-Amz-Algorithm=AWS4-HMAC-SHA256&X-Amz-Credential=AKIAIWNJYAX4CSVEH53A%2F20220614%2Fus-east-1%2Fs3%2Faws4_request&X-Amz-Date=20220614T000536Z&X-Amz-Expires=300&X-Amz-Signature=238f36051ea01c3f5e90af0eedd912c03f7f4e0280c8642b8f16eed6fa829b86&X-Amz-SignedHeaders=host&actor_id=0&key_id=0&repo_id=333825187&response-content-disposition=attachment%3B%20filename%3Dspinalcord_results.zip&response-content-type=application%2Foctet-stream [following]
--2022-06-14 00:05:37--  https://objects.githubusercontent.com/github-production-release-asset-2e65be/333825187/9e444c00-c9e2-11eb-880c-f9aa2a43f100?X-Amz-Algorithm=AWS4-HMAC-SHA256&X-Amz-Credential=AKIAIWNJYAX4CSVEH53A%2F20220614%2Fus-east-1%2Fs3%2Faws4_request&X-Amz-Date=20220614T000536Z&X-Amz-Expires=300&X-Amz-Signature=238f36051ea01c3f5e90af0eedd912c03f7f4e0280c8642b8f16eed6fa829b86&X-Amz-SignedHeaders=host&actor_id=0&key_id=0&repo_id=333825187&response-content-disposition=attachment%3B%20filename%3Dspinalcord_results.zip&response-content-type=application%2Foctet-stream
Resolving objects.githubusercontent.com (objects.githubusercontent.com)... 185.199.110.133, 185.199.109.133, 185.199.108.133, ...
Connecting to objects.githubusercontent.com (objects.githubusercontent.com)|185.199.110.133|:443... connected.
HTTP request sent, awaiting response... 200 OK
Length: 19324 (19K) [application/octet-stream]
Saving to: ‘spinalcord_results.zip’

     0K .......... ........                                   100% 32.1M=0.001s

2022-06-14 00:05:37 (32.1 MB/s) - ‘spinalcord_results.zip’ saved [19324/19324]
dataset.load()

fig_spine = Plot(dataset, plot_name = 'spine-3')
fig_spine.title = 'Spinal cord qMRI microstructure'
matrix = dataset.extract_data('qmri')
print(matrix)
{'DWI_FA':    Subject Session            Timestamp  \
0        1       1  2021-06-09 23:30:45   
5        1       2  2021-06-09 23:31:03   
1        1       3  2021-06-09 23:30:51   
8        2       1  2021-06-09 23:47:07   
9        2       2  2021-06-09 23:47:41   
14       2       3  2021-06-09 23:54:55   
11       2       4  2021-06-09 23:48:00   
10       3       1  2021-06-09 23:47:55   
13       3       2  2021-06-09 23:48:17   
12       3       3  2021-06-09 23:48:06   
15       3       4  2021-06-09 23:59:29   
16       4       2  2021-06-09 23:59:50   
17       4       3  2021-06-10 00:00:01   
4        5       1  2021-06-09 23:30:58   
2        6       1  2021-06-09 23:30:54   
7        6       2  2021-06-09 23:31:06   
6        6       3  2021-06-09 23:31:04   
3        6       4  2021-06-09 23:30:54   

                                          SCT Version  \
0   git-jca/3413-run-batch-session-c41958db922273a...   
5   git-jca/3413-run-batch-session-c41958db922273a...   
1   git-jca/3413-run-batch-session-c41958db922273a...   
8   git-jca/3413-run-batch-session-c41958db922273a...   
9   git-jca/3413-run-batch-session-c41958db922273a...   
14  git-jca/3413-run-batch-session-c41958db922273a...   
11  git-jca/3413-run-batch-session-c41958db922273a...   
10  git-jca/3413-run-batch-session-c41958db922273a...   
13  git-jca/3413-run-batch-session-c41958db922273a...   
12  git-jca/3413-run-batch-session-c41958db922273a...   
15  git-jca/3413-run-batch-session-c41958db922273a...   
16  git-jca/3413-run-batch-session-c41958db922273a...   
17  git-jca/3413-run-batch-session-c41958db922273a...   
4   git-jca/3413-run-batch-session-c41958db922273a...   
2   git-jca/3413-run-batch-session-c41958db922273a...   
7   git-jca/3413-run-batch-session-c41958db922273a...   
6   git-jca/3413-run-batch-session-c41958db922273a...   
3   git-jca/3413-run-batch-session-c41958db922273a...   

                                             Filename Slice (I->S) VertLevel  \
0   /Users/julien/temp/neuromod/data_processed/sub...         0:12       2:5   
5   /Users/julien/temp/neuromod/data_processed/sub...         1:13       2:5   
1   /Users/julien/temp/neuromod/data_processed/sub...         0:13       2:5   
8   /Users/julien/temp/neuromod/data_processed/sub...         1:12       2:5   
9   /Users/julien/temp/neuromod/data_processed/sub...         0:12       2:5   
14  /Users/julien/temp/neuromod/data_processed/sub...         1:12       2:5   
11  /Users/julien/temp/neuromod/data_processed/sub...         1:12       2:5   
10  /Users/julien/temp/neuromod/data_processed/sub...         1:12       2:5   
13  /Users/julien/temp/neuromod/data_processed/sub...         2:12       2:5   
12  /Users/julien/temp/neuromod/data_processed/sub...         2:13       2:5   
15  /Users/julien/temp/neuromod/data_processed/sub...         1:12       2:5   
16  /Users/julien/temp/neuromod/data_processed/sub...         1:12       2:5   
17  /Users/julien/temp/neuromod/data_processed/sub...         2:12       2:5   
4   /Users/julien/temp/neuromod/data_processed/sub...         1:13       2:5   
2   /Users/julien/temp/neuromod/data_processed/sub...         1:12       2:5   
7   /Users/julien/temp/neuromod/data_processed/sub...         1:13       2:5   
6   /Users/julien/temp/neuromod/data_processed/sub...         1:12       2:5   
3   /Users/julien/temp/neuromod/data_processed/sub...         1:13       2:5   

           Label   Size [vox]      WA()     STD()  
0   white matter   904.189345  0.631039  0.140065  
5   white matter   964.007476  0.644994  0.138715  
1   white matter  1039.275888  0.605202  0.148103  
8   white matter  1137.937444  0.799384  0.172222  
9   white matter  1309.761521  0.629431  0.168256  
14  white matter  1153.703857  0.659575  0.162677  
11  white matter  1176.168913  0.717280  0.167405  
10  white matter   768.628748  0.726278  0.148227  
13  white matter   749.162398  0.711276  0.150530  
12  white matter   690.874778  0.478779  0.331780  
15  white matter   778.110046  0.811363  0.142352  
16  white matter   727.057663  0.732361  0.157148  
17  white matter   719.404200  0.722414  0.150972  
4   white matter   952.717593  0.698379  0.169484  
2   white matter   775.946751  0.664973  0.159732  
7   white matter   829.913278  0.688663  0.136988  
6   white matter   757.399533  0.653336  0.154299  
3   white matter   765.939159  0.647316  0.217450  , 'DWI_MD':    Subject Session            Timestamp  \
0        1       1  2021-06-09 23:30:46   
5        1       2  2021-06-09 23:31:05   
1        1       3  2021-06-09 23:30:52   
8        2       1  2021-06-09 23:47:09   
9        2       2  2021-06-09 23:47:42   
14       2       3  2021-06-09 23:54:56   
11       2       4  2021-06-09 23:48:01   
10       3       1  2021-06-09 23:47:57   
13       3       2  2021-06-09 23:48:18   
12       3       3  2021-06-09 23:48:07   
15       3       4  2021-06-09 23:59:30   
16       4       2  2021-06-09 23:59:51   
17       4       3  2021-06-10 00:00:02   
4        5       1  2021-06-09 23:30:59   
2        6       1  2021-06-09 23:30:55   
7        6       2  2021-06-09 23:31:07   
6        6       3  2021-06-09 23:31:05   
3        6       4  2021-06-09 23:30:55   

                                          SCT Version  \
0   git-jca/3413-run-batch-session-c41958db922273a...   
5   git-jca/3413-run-batch-session-c41958db922273a...   
1   git-jca/3413-run-batch-session-c41958db922273a...   
8   git-jca/3413-run-batch-session-c41958db922273a...   
9   git-jca/3413-run-batch-session-c41958db922273a...   
14  git-jca/3413-run-batch-session-c41958db922273a...   
11  git-jca/3413-run-batch-session-c41958db922273a...   
10  git-jca/3413-run-batch-session-c41958db922273a...   
13  git-jca/3413-run-batch-session-c41958db922273a...   
12  git-jca/3413-run-batch-session-c41958db922273a...   
15  git-jca/3413-run-batch-session-c41958db922273a...   
16  git-jca/3413-run-batch-session-c41958db922273a...   
17  git-jca/3413-run-batch-session-c41958db922273a...   
4   git-jca/3413-run-batch-session-c41958db922273a...   
2   git-jca/3413-run-batch-session-c41958db922273a...   
7   git-jca/3413-run-batch-session-c41958db922273a...   
6   git-jca/3413-run-batch-session-c41958db922273a...   
3   git-jca/3413-run-batch-session-c41958db922273a...   

                                             Filename Slice (I->S) VertLevel  \
0   /Users/julien/temp/neuromod/data_processed/sub...         0:12       2:5   
5   /Users/julien/temp/neuromod/data_processed/sub...         1:13       2:5   
1   /Users/julien/temp/neuromod/data_processed/sub...         0:13       2:5   
8   /Users/julien/temp/neuromod/data_processed/sub...         1:12       2:5   
9   /Users/julien/temp/neuromod/data_processed/sub...         0:12       2:5   
14  /Users/julien/temp/neuromod/data_processed/sub...         1:12       2:5   
11  /Users/julien/temp/neuromod/data_processed/sub...         1:12       2:5   
10  /Users/julien/temp/neuromod/data_processed/sub...         1:12       2:5   
13  /Users/julien/temp/neuromod/data_processed/sub...         2:12       2:5   
12  /Users/julien/temp/neuromod/data_processed/sub...         2:13       2:5   
15  /Users/julien/temp/neuromod/data_processed/sub...         1:12       2:5   
16  /Users/julien/temp/neuromod/data_processed/sub...         1:12       2:5   
17  /Users/julien/temp/neuromod/data_processed/sub...         2:12       2:5   
4   /Users/julien/temp/neuromod/data_processed/sub...         1:13       2:5   
2   /Users/julien/temp/neuromod/data_processed/sub...         1:12       2:5   
7   /Users/julien/temp/neuromod/data_processed/sub...         1:13       2:5   
6   /Users/julien/temp/neuromod/data_processed/sub...         1:12       2:5   
3   /Users/julien/temp/neuromod/data_processed/sub...         1:13       2:5   

           Label   Size [vox]      WA()     STD()  
0   white matter   904.189345  0.001014  0.000219  
5   white matter   964.007476  0.001018  0.000229  
1   white matter  1039.275888  0.001026  0.000231  
8   white matter  1137.937444  0.001401  0.000837  
9   white matter  1309.761521  0.000976  0.000264  
14  white matter  1153.703857  0.000912  0.000219  
11  white matter  1176.168913  0.000815  0.000253  
10  white matter   768.628748  0.000961  0.000256  
13  white matter   749.162398  0.000991  0.000267  
12  white matter   690.874778  0.000669  0.000551  
15  white matter   778.110046  0.000894  0.000252  
16  white matter   727.057663  0.000965  0.000282  
17  white matter   719.404200  0.001035  0.000284  
4   white matter   952.717593  0.000977  0.000306  
2   white matter   775.946751  0.001055  0.000249  
7   white matter   829.913278  0.001012  0.000252  
6   white matter   757.399533  0.001018  0.000244  
3   white matter   765.939159  0.000917  0.000348  , 'DWI_RD':    Subject Session            Timestamp  \
0        1       1  2021-06-09 23:30:47   
5        1       2  2021-06-09 23:31:06   
1        1       3  2021-06-09 23:30:53   
8        2       1  2021-06-09 23:47:10   
9        2       2  2021-06-09 23:47:43   
14       2       3  2021-06-09 23:54:57   
11       2       4  2021-06-09 23:48:02   
10       3       1  2021-06-09 23:47:59   
13       3       2  2021-06-09 23:48:19   
12       3       3  2021-06-09 23:48:08   
15       3       4  2021-06-09 23:59:31   
16       4       2  2021-06-09 23:59:52   
17       4       3  2021-06-10 00:00:02   
4        5       1  2021-06-09 23:31:00   
2        6       1  2021-06-09 23:30:56   
7        6       2  2021-06-09 23:31:08   
6        6       3  2021-06-09 23:31:06   
3        6       4  2021-06-09 23:30:57   

                                          SCT Version  \
0   git-jca/3413-run-batch-session-c41958db922273a...   
5   git-jca/3413-run-batch-session-c41958db922273a...   
1   git-jca/3413-run-batch-session-c41958db922273a...   
8   git-jca/3413-run-batch-session-c41958db922273a...   
9   git-jca/3413-run-batch-session-c41958db922273a...   
14  git-jca/3413-run-batch-session-c41958db922273a...   
11  git-jca/3413-run-batch-session-c41958db922273a...   
10  git-jca/3413-run-batch-session-c41958db922273a...   
13  git-jca/3413-run-batch-session-c41958db922273a...   
12  git-jca/3413-run-batch-session-c41958db922273a...   
15  git-jca/3413-run-batch-session-c41958db922273a...   
16  git-jca/3413-run-batch-session-c41958db922273a...   
17  git-jca/3413-run-batch-session-c41958db922273a...   
4   git-jca/3413-run-batch-session-c41958db922273a...   
2   git-jca/3413-run-batch-session-c41958db922273a...   
7   git-jca/3413-run-batch-session-c41958db922273a...   
6   git-jca/3413-run-batch-session-c41958db922273a...   
3   git-jca/3413-run-batch-session-c41958db922273a...   

                                             Filename Slice (I->S) VertLevel  \
0   /Users/julien/temp/neuromod/data_processed/sub...         0:12       2:5   
5   /Users/julien/temp/neuromod/data_processed/sub...         1:13       2:5   
1   /Users/julien/temp/neuromod/data_processed/sub...         0:13       2:5   
8   /Users/julien/temp/neuromod/data_processed/sub...         1:12       2:5   
9   /Users/julien/temp/neuromod/data_processed/sub...         0:12       2:5   
14  /Users/julien/temp/neuromod/data_processed/sub...         1:12       2:5   
11  /Users/julien/temp/neuromod/data_processed/sub...         1:12       2:5   
10  /Users/julien/temp/neuromod/data_processed/sub...         1:12       2:5   
13  /Users/julien/temp/neuromod/data_processed/sub...         2:12       2:5   
12  /Users/julien/temp/neuromod/data_processed/sub...         2:13       2:5   
15  /Users/julien/temp/neuromod/data_processed/sub...         1:12       2:5   
16  /Users/julien/temp/neuromod/data_processed/sub...         1:12       2:5   
17  /Users/julien/temp/neuromod/data_processed/sub...         2:12       2:5   
4   /Users/julien/temp/neuromod/data_processed/sub...         1:13       2:5   
2   /Users/julien/temp/neuromod/data_processed/sub...         1:12       2:5   
7   /Users/julien/temp/neuromod/data_processed/sub...         1:13       2:5   
6   /Users/julien/temp/neuromod/data_processed/sub...         1:12       2:5   
3   /Users/julien/temp/neuromod/data_processed/sub...         1:13       2:5   

           Label   Size [vox]      WA()     STD()  
0   white matter   904.189345  0.000594  0.000228  
5   white matter   964.007476  0.000596  0.000245  
1   white matter  1039.275888  0.000627  0.000251  
8   white matter  1137.937444  0.000511  0.000302  
9   white matter  1309.761521  0.000570  0.000273  
14  white matter  1153.703857  0.000514  0.000236  
11  white matter  1176.168913  0.000414  0.000264  
10  white matter   768.628748  0.000467  0.000282  
13  white matter   749.162398  0.000503  0.000295  
12  white matter   690.874778  0.000407  0.000431  
15  white matter   778.110046  0.000339  0.000270  
16  white matter   727.057663  0.000469  0.000321  
17  white matter   719.404200  0.000512  0.000318  
4   white matter   952.717593  0.000505  0.000271  
2   white matter   775.946751  0.000578  0.000283  
7   white matter   829.913278  0.000532  0.000249  
6   white matter   757.399533  0.000573  0.000268  
3   white matter   765.939159  0.000494  0.000287  , 'MTR':    Subject Session            Timestamp  \
0        1       1  2021-06-09 23:26:40   
5        1       2  2021-06-09 23:26:51   
1        1       3  2021-06-09 23:26:41   
8        2       1  2021-06-09 23:43:47   
9        2       2  2021-06-09 23:43:58   
15       2       3  2021-06-09 23:52:31   
11       2       4  2021-06-09 23:44:09   
10       3       1  2021-06-09 23:44:06   
13       3       2  2021-06-09 23:44:37   
12       3       3  2021-06-09 23:44:25   
16       3       4  2021-06-09 23:57:07   
17       4       2  2021-06-09 23:57:33   
18       4       3  2021-06-09 23:57:45   
4        5       1  2021-06-09 23:26:48   
14       5       2  2021-06-09 23:47:18   
2        6       1  2021-06-09 23:26:44   
7        6       2  2021-06-09 23:26:56   
6        6       3  2021-06-09 23:26:53   
3        6       4  2021-06-09 23:26:46   

                                          SCT Version  \
0   git-jca/3413-run-batch-session-c41958db922273a...   
5   git-jca/3413-run-batch-session-c41958db922273a...   
1   git-jca/3413-run-batch-session-c41958db922273a...   
8   git-jca/3413-run-batch-session-c41958db922273a...   
9   git-jca/3413-run-batch-session-c41958db922273a...   
15  git-jca/3413-run-batch-session-c41958db922273a...   
11  git-jca/3413-run-batch-session-c41958db922273a...   
10  git-jca/3413-run-batch-session-c41958db922273a...   
13  git-jca/3413-run-batch-session-c41958db922273a...   
12  git-jca/3413-run-batch-session-c41958db922273a...   
16  git-jca/3413-run-batch-session-c41958db922273a...   
17  git-jca/3413-run-batch-session-c41958db922273a...   
18  git-jca/3413-run-batch-session-c41958db922273a...   
4   git-jca/3413-run-batch-session-c41958db922273a...   
14  git-jca/3413-run-batch-session-c41958db922273a...   
2   git-jca/3413-run-batch-session-c41958db922273a...   
7   git-jca/3413-run-batch-session-c41958db922273a...   
6   git-jca/3413-run-batch-session-c41958db922273a...   
3   git-jca/3413-run-batch-session-c41958db922273a...   

                                             Filename Slice (I->S) VertLevel  \
0   /Users/julien/temp/neuromod/data_processed/sub...         0:13       2:5   
5   /Users/julien/temp/neuromod/data_processed/sub...         2:15       2:5   
1   /Users/julien/temp/neuromod/data_processed/sub...         3:16       2:5   
8   /Users/julien/temp/neuromod/data_processed/sub...         1:12       2:5   
9   /Users/julien/temp/neuromod/data_processed/sub...         1:13       2:5   
15  /Users/julien/temp/neuromod/data_processed/sub...         1:12       2:5   
11  /Users/julien/temp/neuromod/data_processed/sub...         0:11       2:5   
10  /Users/julien/temp/neuromod/data_processed/sub...         5:16       2:5   
13  /Users/julien/temp/neuromod/data_processed/sub...         5:15       2:5   
12  /Users/julien/temp/neuromod/data_processed/sub...         4:15       2:5   
16  /Users/julien/temp/neuromod/data_processed/sub...         5:15       2:5   
17  /Users/julien/temp/neuromod/data_processed/sub...         5:15       2:5   
18  /Users/julien/temp/neuromod/data_processed/sub...         4:15       2:5   
4   /Users/julien/temp/neuromod/data_processed/sub...         1:13       2:5   
14  /Users/julien/temp/neuromod/data_processed/sub...       85:156       2:5   
2   /Users/julien/temp/neuromod/data_processed/sub...         4:16       2:5   
7   /Users/julien/temp/neuromod/data_processed/sub...         4:15       2:5   
6   /Users/julien/temp/neuromod/data_processed/sub...         3:15       2:5   
3   /Users/julien/temp/neuromod/data_processed/sub...         5:17       2:5   

           Label   Size [vox]       WA()      STD()  
0   white matter  1046.054370  44.209522   5.546168  
5   white matter  1018.908949  50.699601   3.897717  
1   white matter  1041.891840  45.682771   4.558806  
8   white matter  1115.519208  42.679169  13.292257  
9   white matter  1195.521827  37.822614   8.048927  
15  white matter  1117.192721  44.258456   8.416986  
11  white matter  1056.832881  40.766881  10.644967  
10  white matter   804.568625  47.497072   4.550398  
13  white matter   746.026673  47.810683   5.161154  
12  white matter   777.814473  47.573785   4.537513  
16  white matter   720.962692  47.197086   5.450475  
17  white matter   731.762283  46.773349   4.927121  
18  white matter   812.075778  47.797203   4.550833  
4   white matter   968.164278  46.802710   9.793295  
14  white matter   826.424784  44.272382   7.513139  
2   white matter   847.472701  47.150662   4.334012  
7   white matter   790.522420  46.347500   6.902517  
6   white matter   845.598555  48.022072   6.061917  
3   white matter   856.011955  45.055435   5.637046  , 'MTSat':    Subject Session            Timestamp  \
0        1       1  2021-06-09 23:26:42   
5        1       2  2021-06-09 23:26:52   
1        1       3  2021-06-09 23:26:42   
8        2       1  2021-06-09 23:43:48   
9        2       2  2021-06-09 23:43:59   
15       2       3  2021-06-09 23:52:32   
11       2       4  2021-06-09 23:44:10   
10       3       1  2021-06-09 23:44:07   
13       3       2  2021-06-09 23:44:39   
12       3       3  2021-06-09 23:44:27   
16       3       4  2021-06-09 23:57:08   
17       4       2  2021-06-09 23:57:35   
18       4       3  2021-06-09 23:57:46   
4        5       1  2021-06-09 23:26:49   
14       5       2  2021-06-09 23:47:19   
2        6       1  2021-06-09 23:26:45   
7        6       2  2021-06-09 23:26:57   
6        6       3  2021-06-09 23:26:54   
3        6       4  2021-06-09 23:26:48   

                                          SCT Version  \
0   git-jca/3413-run-batch-session-c41958db922273a...   
5   git-jca/3413-run-batch-session-c41958db922273a...   
1   git-jca/3413-run-batch-session-c41958db922273a...   
8   git-jca/3413-run-batch-session-c41958db922273a...   
9   git-jca/3413-run-batch-session-c41958db922273a...   
15  git-jca/3413-run-batch-session-c41958db922273a...   
11  git-jca/3413-run-batch-session-c41958db922273a...   
10  git-jca/3413-run-batch-session-c41958db922273a...   
13  git-jca/3413-run-batch-session-c41958db922273a...   
12  git-jca/3413-run-batch-session-c41958db922273a...   
16  git-jca/3413-run-batch-session-c41958db922273a...   
17  git-jca/3413-run-batch-session-c41958db922273a...   
18  git-jca/3413-run-batch-session-c41958db922273a...   
4   git-jca/3413-run-batch-session-c41958db922273a...   
14  git-jca/3413-run-batch-session-c41958db922273a...   
2   git-jca/3413-run-batch-session-c41958db922273a...   
7   git-jca/3413-run-batch-session-c41958db922273a...   
6   git-jca/3413-run-batch-session-c41958db922273a...   
3   git-jca/3413-run-batch-session-c41958db922273a...   

                                             Filename Slice (I->S) VertLevel  \
0   /Users/julien/temp/neuromod/data_processed/sub...         0:13       2:5   
5   /Users/julien/temp/neuromod/data_processed/sub...         2:15       2:5   
1   /Users/julien/temp/neuromod/data_processed/sub...         3:16       2:5   
8   /Users/julien/temp/neuromod/data_processed/sub...         1:12       2:5   
9   /Users/julien/temp/neuromod/data_processed/sub...         1:13       2:5   
15  /Users/julien/temp/neuromod/data_processed/sub...         1:12       2:5   
11  /Users/julien/temp/neuromod/data_processed/sub...         0:11       2:5   
10  /Users/julien/temp/neuromod/data_processed/sub...         5:16       2:5   
13  /Users/julien/temp/neuromod/data_processed/sub...         5:15       2:5   
12  /Users/julien/temp/neuromod/data_processed/sub...         4:15       2:5   
16  /Users/julien/temp/neuromod/data_processed/sub...         5:15       2:5   
17  /Users/julien/temp/neuromod/data_processed/sub...         5:15       2:5   
18  /Users/julien/temp/neuromod/data_processed/sub...         4:15       2:5   
4   /Users/julien/temp/neuromod/data_processed/sub...         1:13       2:5   
14  /Users/julien/temp/neuromod/data_processed/sub...       85:156       2:5   
2   /Users/julien/temp/neuromod/data_processed/sub...         4:16       2:5   
7   /Users/julien/temp/neuromod/data_processed/sub...         4:15       2:5   
6   /Users/julien/temp/neuromod/data_processed/sub...         3:15       2:5   
3   /Users/julien/temp/neuromod/data_processed/sub...         5:17       2:5   

           Label   Size [vox]      WA()     STD()  
0   white matter  1046.054370  3.499266  1.451179  
5   white matter  1018.908949  3.806936  0.718392  
1   white matter  1041.891840  3.357581  0.632779  
8   white matter  1115.519208  3.855797  3.086657  
9   white matter  1195.521827  2.846363  0.918702  
15  white matter  1117.192721  4.075625  1.419094  
11  white matter  1056.832881  3.373417  1.332627  
10  white matter   804.568625  3.724485  0.733619  
13  white matter   746.026673  3.704875  0.788456  
12  white matter   777.814473  3.589619  0.696303  
16  white matter   720.962692  3.442284  0.677691  
17  white matter   731.762283  3.539466  0.728657  
18  white matter   812.075778  3.637116  0.735389  
4   white matter   968.164278  3.576086  1.190436  
14  white matter   826.424784  3.313316  1.291342  
2   white matter   847.472701  3.739600  0.735669  
7   white matter   790.522420  3.573418  0.871603  
6   white matter   845.598555  4.034849  1.202511  
3   white matter   856.011955  3.467103  0.859480  , 'T1':    Subject Session            Timestamp  \
0        1       1  2021-06-09 23:26:43   
5        1       2  2021-06-09 23:26:53   
1        1       3  2021-06-09 23:26:43   
8        2       1  2021-06-09 23:43:49   
9        2       2  2021-06-09 23:44:00   
15       2       3  2021-06-09 23:52:33   
11       2       4  2021-06-09 23:44:11   
10       3       1  2021-06-09 23:44:08   
13       3       2  2021-06-09 23:44:41   
12       3       3  2021-06-09 23:44:28   
16       3       4  2021-06-09 23:57:09   
17       4       2  2021-06-09 23:57:36   
18       4       3  2021-06-09 23:57:46   
4        5       1  2021-06-09 23:26:50   
14       5       2  2021-06-09 23:47:20   
2        6       1  2021-06-09 23:26:46   
7        6       2  2021-06-09 23:26:58   
6        6       3  2021-06-09 23:26:55   
3        6       4  2021-06-09 23:26:49   

                                          SCT Version  \
0   git-jca/3413-run-batch-session-c41958db922273a...   
5   git-jca/3413-run-batch-session-c41958db922273a...   
1   git-jca/3413-run-batch-session-c41958db922273a...   
8   git-jca/3413-run-batch-session-c41958db922273a...   
9   git-jca/3413-run-batch-session-c41958db922273a...   
15  git-jca/3413-run-batch-session-c41958db922273a...   
11  git-jca/3413-run-batch-session-c41958db922273a...   
10  git-jca/3413-run-batch-session-c41958db922273a...   
13  git-jca/3413-run-batch-session-c41958db922273a...   
12  git-jca/3413-run-batch-session-c41958db922273a...   
16  git-jca/3413-run-batch-session-c41958db922273a...   
17  git-jca/3413-run-batch-session-c41958db922273a...   
18  git-jca/3413-run-batch-session-c41958db922273a...   
4   git-jca/3413-run-batch-session-c41958db922273a...   
14  git-jca/3413-run-batch-session-c41958db922273a...   
2   git-jca/3413-run-batch-session-c41958db922273a...   
7   git-jca/3413-run-batch-session-c41958db922273a...   
6   git-jca/3413-run-batch-session-c41958db922273a...   
3   git-jca/3413-run-batch-session-c41958db922273a...   

                                             Filename Slice (I->S) VertLevel  \
0   /Users/julien/temp/neuromod/data_processed/sub...         0:13       2:5   
5   /Users/julien/temp/neuromod/data_processed/sub...         2:15       2:5   
1   /Users/julien/temp/neuromod/data_processed/sub...         3:16       2:5   
8   /Users/julien/temp/neuromod/data_processed/sub...         1:12       2:5   
9   /Users/julien/temp/neuromod/data_processed/sub...         1:13       2:5   
15  /Users/julien/temp/neuromod/data_processed/sub...         1:12       2:5   
11  /Users/julien/temp/neuromod/data_processed/sub...         0:11       2:5   
10  /Users/julien/temp/neuromod/data_processed/sub...         5:16       2:5   
13  /Users/julien/temp/neuromod/data_processed/sub...         5:15       2:5   
12  /Users/julien/temp/neuromod/data_processed/sub...         4:15       2:5   
16  /Users/julien/temp/neuromod/data_processed/sub...         5:15       2:5   
17  /Users/julien/temp/neuromod/data_processed/sub...         5:15       2:5   
18  /Users/julien/temp/neuromod/data_processed/sub...         4:15       2:5   
4   /Users/julien/temp/neuromod/data_processed/sub...         1:13       2:5   
14  /Users/julien/temp/neuromod/data_processed/sub...       85:156       2:5   
2   /Users/julien/temp/neuromod/data_processed/sub...         4:16       2:5   
7   /Users/julien/temp/neuromod/data_processed/sub...         4:15       2:5   
6   /Users/julien/temp/neuromod/data_processed/sub...         3:15       2:5   
3   /Users/julien/temp/neuromod/data_processed/sub...         5:17       2:5   

           Label   Size [vox]      WA()     STD()  
0   white matter  1046.054370  0.001292  0.000386  
5   white matter  1018.908949  0.001484  0.000239  
1   white matter  1041.891840  0.001337  0.000263  
8   white matter  1115.519208  0.001139  0.000765  
9   white matter  1195.521827  0.001123  0.000304  
15  white matter  1117.192721  0.001036  0.000347  
11  white matter  1056.832881  0.001098  0.000357  
10  white matter   804.568625  0.001277  0.000228  
13  white matter   746.026673  0.001316  0.000233  
12  white matter   777.814473  0.001354  0.000246  
16  white matter   720.962692  0.001415  0.000263  
17  white matter   731.762283  0.001323  0.000242  
18  white matter   812.075778  0.001350  0.000258  
4   white matter   968.164278  0.001627  0.008498  
14  white matter   826.424784  0.001381  0.000426  
2   white matter   847.472701  0.001240  0.000209  
7   white matter   790.522420  0.001302  0.000295  
6   white matter   845.598555  0.001223  0.000280  
3   white matter   856.011955  0.001256  0.000262  }
{'DWI_FA': [[0.6310385280039796, 0.6449939742310774, 0.6052019869249001, 0.6052019869249001], [0.799384499868077, 0.6294310187889507, 0.6595746693454234, 0.7172795640397259], [0.7262775593497328, 0.7112761015883302, 0.4787790887981428, 0.8113632640960852], [0.8113632640960852, 0.7323609952753036, 0.7224137607034387, 0.7224137607034387], [0.6983788722936425, 0.6983788722936425, 0.6983788722936425, 0.6983788722936425], [0.6649732448837092, 0.688663199247152, 0.6533355425960395, 0.6473157034113586]], 'DWI_MD': [[0.0010138856451204, 0.0010177543993774, 0.0010257196398529, 0.0010257196398529], [0.0014014718331852, 0.0009761721717434, 0.0009117604540341, 0.000815311519069], [0.0009605911746559, 0.0009906206359397, 0.0006694445137909, 0.0008935883019168], [0.0008935883019168, 0.0009645148099392, 0.0010351902433702, 0.0010351902433702], [0.0009774778167169, 0.0009774778167169, 0.0009774778167169, 0.0009774778167169], [0.0010551867192628, 0.001012210010244, 0.0010180580331023, 0.0009165329349018]], 'DWI_RD': [[0.0005942976466395, 0.0005960152894725, 0.00062691302888, 0.00062691302888], [0.0005112709262059, 0.0005704880839017, 0.0005137069084603, 0.0004143742226968], [0.0004672565333558, 0.0005026007210642, 0.0004066867643462, 0.0003393328073422], [0.0003393328073422, 0.0004692023931709, 0.0005123971557951, 0.0005123971557951], [0.0005045102052002, 0.0005045102052002, 0.0005045102052002, 0.0005045102052002], [0.000577999230138, 0.0005316527869437, 0.0005729917043376, 0.0004937373474434]], 'MTR': [[44.209522055240505, 50.69960144846205, 45.682771475180594, 45.682771475180594], [42.67916913302598, 37.82261433907465, 44.258456219263856, 40.76688074907387], [47.497071935829645, 47.81068337186637, 47.57378502229639, 47.19708621549288], [47.19708621549288, 46.77334882206762, 47.79720317144616, 47.79720317144616], [46.802709566692286, 44.27238222794652, 44.27238222794652, 44.27238222794652], [47.15066198433709, 46.34750036374999, 48.02207246120396, 45.055435263858136]], 'MTSat': [[3.499265814909754, 3.80693641422522, 3.3575814030216278, 3.3575814030216278], [3.8557974910487354, 2.846363452702357, 4.075625383910599, 3.373417235607917], [3.7244854393057487, 3.704874827322425, 3.589619356583784, 3.442284461661099], [3.442284461661099, 3.539465912889603, 3.637115993665185, 3.637115993665185], [3.576085608246151, 3.313315766455653, 3.313315766455653, 3.313315766455653], [3.739600198542477, 3.5734180021212527, 4.034849342197791, 3.4671027317089025]], 'T1': [[0.00129223798176, 0.0014841752890748, 0.0013368451408746, 0.0013368451408746], [0.0011388416775548, 0.001123306492997, 0.001036083901409, 0.0010984101977734], [0.0012773608831078, 0.0013156767241556, 0.0013540267986507, 0.0014153027257222], [0.0014153027257222, 0.0013227935588819, 0.0013498186815148, 0.0013498186815148], [0.0016271384699499, 0.0013811508940738, 0.0013811508940738, 0.0013811508940738], [0.0012395962831586, 0.0013018090136284, 0.0012232588411571, 0.0012559476536657]]}
# If you're running this notebook in a Jupyter Notebook (eg, on MyBinder), change 'jupyter-book' to 'notebook'
#fig_spine.display('jupyter-book', tissue = 'qMRI')